GBS paired reads splits it into several smaller files based on barcode matching
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4.9 years ago

I wanted to split demultiplexed paired-end Fastq files into individual data based on barcode matching. I know that single-end reads could be divided using FASTX-Toolkit, but not paired-end reads. Please tell me how to split demultiplexed paired-end Fastq files. Only R1 reads contain the barcode.

next-gen sequencing • 1.8k views
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did you try GBSX tool? nakanomasayuki265

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2.9 years ago
rimgubaev ▴ 270

Actually, I am dealing with the same problem, can't find a proper solution. I found this package but didn't try it yet: https://sourceforge.net/projects/gbsbarcode/files/

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2.9 years ago
Corentin ▴ 480

I used this tool before to split GBS reads: https://sourceforge.net/projects/gbsbarcode/

It support paired end reads

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2.9 years ago
rimgubaev ▴ 270

Tried this tool: https://github.com/kdmurray91/axe Works fine!

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